Biology Theses and Dissertations
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Item PROBIOTIC, PREBIOTIC, AND SYNBIOTIC APPROACHES IN SUSTAINABLE POULTRY PRODUCTION THROUGH MICROBIOME MODULATION(2023) Tabashsum, Zajeba; Biswas, Debabrata; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Campylobacter is one of the prominent causative agents of acute gastroenteritis in the US and more than 70% of Campylobacter infections, known as Campylobacteriosis, are occurred through raw or undercooked poultry consumption or improper handling of contaminated poultry products. Moreover, reports show that the antibiotic resistance pattern of Campylobacter is persistent and in the absence of sub-therapeutic antibiotic growth promoter, colonization of this bacterial pathogen in poultry gut or on skin and the potential risk of cross-contamination of the finished poultry products are increasing, Therefore, both conventional and organic/pasture poultry farmers are searching for sustainable alternative to synthetic antibiotics which can reduce colonization and cross-contamination of poultry products with poultry-borne bacterial pathogens specifically Campylobacter. On the other hand, due to the consumers’ demand, majority poultry farmers are growing their chicks without sub-therapeutic growth promotor which leads to slow growth and higher mortality rates. Therefore, to make the poultry farming sustainable, farmers need alternative feed or water supplement which can promote poultry health and growth. Probiotics, prebiotics, or a combination of these two referred to as synbiotics, have emerged as a promising natural and alternative approach to sustainable animal farming. Probiotics and their metabolites such as conjugated linoleic acids (CLAs) play a crucial role in improving host health and act as antimicrobials against enteric pathogens. Our lab developed a genetically engineered probiotic, LC+mcra that can convert more CLA by over-expressing the mcra (myosin-cross-reactive-antigen) in Lactobacillus casei (LC). Further, prebiotic-like components such as bioactive phenolic extracts (BPEs) from berry pomace can stimulate the growth of beneficial microbes including LC, competitively inhibit growth of enteric bacterial pathogens, and promote the growth of chickens in a concentration-dependent manner when applied throughout the growth period. In our previous study, we observed that LC+mcra effectively eliminated Campylobacter jejuni (CJ) in co-culture condition as well as the cell free culture supernatants (CFCS) of LC+mcra was effective in growth reduction of CJ. LC+mcra and its CFCSs also reduced the adherence and invasion ability of CJ to both HD-11 and HeLa cells. Physicochemical properties and gene expressions related to CJ virulence were also altered by CFCSs treatments. These findings suggested, LC+mcra can be an alternative in controlling CJ growth along with other beneficial attributes of LC. Then, we aimed to enhance the efficiency of antimicrobial/beneficial activities of LC+mcra by combining BPEs. In mixed culture condition, LC+mcra in the presence of BPE reduced the growth of CJ more efficiently as well as the CFCS of LC+mcra in the presence of BPE. Interaction of CJ with cultured DF-1, HD-11, and HeLa were altered significantly. Further, combined treatments altered the physicochemical properties and expression of multiple virulence genes such as ciaB, cdtB, cadF, flaA, flaB of CJ. This finding indicates that BPE and LC+mcra in combination might be able to prevent colonization of CJ in poultry. So, in our present study at simulated gut conditions, we evaluated combined effect of LC+mcra and BPE in reducing growth of Campylobacter in cecum contents. Cecum contents were collected from chickens pre-inoculated with kanamycin resistant CJ (CJ-Km), incubated over 48h time period, while being supplemented with either BPE, CFCS from LC+mcra, or their combination. It was found that combined treatments were able to reduce both inoculated and naturally colonized Campylobacter more effectively. Microbiome analysis using 16S rRNA sequencing also revealed that combined treatments were capable of altering natural microflora positively within chicken cecum contents. Then, the effect of sustainable probiotics on CJ colonization and gut microbiome composition was evaluated using chicken as a model. A total of 120 chickens were used in duplicate trials to investigate the effectiveness of LC+mcra in decreasing CJ colonization by means of CJ-Km compared to the control group. We observed that LC+mcra could efficiently colonize various parts of the chicken gut and competitively reduce colonization of natural and challenged Campylobacter. Furthermore, 16S rRNA compositional analysis revealed lower abundance of Proteobacteria, higher abundance of Firmicutes, along with enriched bacterial genus diversity in gut of LC+mcra fed chicken. Outcomes of this study reveal high potential of LC+mcra as sustainable approach to decrease colonization of Campylobacter in poultry gut along with other beneficial attributes. So, we further evaluated the combined effect of LC+mcra and a low dose of BPE on Campylobacter colonization in chicken gut using a day-old chick model. Colonization of CJ-Km as well as the natural colonization of Campylobacter was reduced by the combined effect of LC+mcra and BPEs significantly at all time points. In the cecum contents of the LC+mcra and BPEs treatment group, there was notable change at phylum level microbiome compared to the control group. At genus level colonization of Lactobacillus was significantly higher (1.7 folds), Campylobacter colonization was reduced significantly (6.3 folds), and other microflora remained balanced due to the combined treatment of LC+mcra and BPEs. Therefore, LC+mcra with BPEs could be an alternative to improve the safety of poultry products and reduce campylobacteriosis in humans sustainably. The application period of this synbiotic compositions could be extended to improve the poultry growth rate as an additional benefit of the LC+mcra and BPEs.Item DIVERGENT MATING STRATEGIES ACROSS THE PEROMYSCUS GENUS DRIVE REPRODUCTIVE TRAIT DIVERSITY(2022) Weber, William David; Fisher, Heidi S; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The study of sexual selection and reproductive biology are dynamic research fields that contribute to basic research, public health, agriculture, and conservation. Peromyscus mice are an important model for studying the evolution of reproductive traits shaped by sexual selection due to the natural diversity of mating systems in this genus. Like most rodents, the ancestral mating strategy of Peromyscus is believed to be promiscuity, but monogamy has evolved independently at least twice. In this dissertation, I investigate how the divergent mating systems in Peromyscus have shaped the diversity of reproductive traits using six species (three monogamous and three promiscuous). First, I characterize the estrous cycle and show that promiscuous species display more intense estrous signaling than monogamous species, but I find a uniform cycle length across the genus. Moreover, I report a method to hormonally-induce ovulation in two species, P. polionotus (monogamous) and P. maniculatus (promiscuous). Second, to investigate the co-evolution of male and female reproductive traits, I examined six species that have evolved under divergent sexual selection pressures and found a correlated expression of traits associated with sperm competition in males and control of fertilization in females. Third, I focus again on P. polionotus and P. maniculatus to examine how mating system influences male response to perceived competition for reproductive success using resident-intruder introductions. I found that while the males of monogamous species were highly aggressive toward rivals, the promiscuous species increased sperm production, which is predicted to increase fertilization success when females mate multiply. Together, this research both characterizes and functionally tests how evolutionary history and social interactions have shaped the diversity in reproductive traits of Peromyscus mice.Item EXAMINING THE GENETIC BASIS AND PHYSIOLOGY OF SURVIVAL IN EXTREME LOW SALINITY TO IMPROVE AQUACULTURE OF THE EASTERN OYSTER Crassostrea virginica(2022) McCarty, Alexandra J; Plough, Louis; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The eastern oyster, Crassostrea virginica, is an important aquaculture species and supports a growing industry along the east coast of the United States. However, increases in freshwater from storm events and intentional diversions can expose coastal aquaculture operations to extreme low salinity (< 5), resulting in reduced productivity and mortality. The primary objectives of this dissertation were to investigate the biology and genetic basis of low salinity tolerance to improve eastern oyster aquaculture. In Chapter 2, I developed and conducted a series of extreme low salinity (2.5) challenges to estimate the quantitative genetic parameters of low salinity survival. A moderate narrow-sense heritability was estimated for challenge survival, h2 ≈ 0.4. In addition, osmolality of hemolymph collected from oysters during the first week of the challenge suggest that all individuals conformed to the surrounding low salinity regardless of challenge survival. In Chapter 3, I performed additional low salinity challenges to assess the importance of challenge duration (2 or 6 months) and temperature (chronic or fluctuating) on low salinity survival. I also investigated algae removal during the chronic challenge to better understand oyster response during low salinity stress. Phenotypic (rS = 0.89) and genetic (rG = 0.81) correlations between family mortality were high across the two challenges, indicating that a 30-day exposure at a constant low salinity (2.5) and temperature (27°C) is a sufficient progeny test for low salinity survival. Modest associations between algae removal metrics and survival in extreme low salinity indicate that individual feeding ability may relate to differential low salinity survival. Lastly, in Chapter 4, I performed genome mapping to investigate the genomic architecture of low salinity survival. Quantitative trait locus mapping and linkage disequilibrium analysis revealed a significant region on eastern oyster chromosome 1 and 7. Genomic prediction accuracies for survival and day to death in extreme low salinity were moderate and encouraging, 0.49 – 0.57. The results from my dissertation characterize the genetic basis of survival during low salinity events and support the incorporation of this trait into breeding efforts to improve production and enhance the resiliency of the eastern oyster aquaculture industry.Item The use of the domestic dog (Canis familiaris) as a comparative model for speech perception(2020) Mallikarjun, Amritha; Newman, Rochelle S; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Animals have long been used as comparative models for adult human speech perception. However, few animal models have been used to explore developmental speech perception questions. This dissertation encourages the use of domestic dogs as a behavioral model for speech perception processes. Specifically, dog models are suggested for questions about 1) the role and function of underlying processes responsible for different aspects of speech perception, and 2) the effect of language experience on speech perception processes. Chapters 2, 3, and 4 examined the contributions of auditory, attention, and linguistic processing skills to infants’ difficulties understanding speech in noise. It is not known why infants have more difficulties perceiving speech in noise, especially single-talker noise, than adults. Understanding speech in noise relies on infants’ auditory, attention, and linguistic processes. It is methodologically difficult to isolate these systems’ contributions when testing infants. To tease apart these systems, I compared dogs’ name recognition in nine- and single-talker background noise to that of infants. These studies suggest that attentional processes play a large role in infants’ difficulties in understanding speech in noise. Chapter 5 explored the reasons behind infants’ shift from a preference for vowel information (vowel bias) to consonant information (consonant bias) in word identification. This shift may occur due to language exposure, or possessing a particular lexicon size and structure. To better understand the linguistic exposure necessary for consonant bias development, I tested dogs, who have long-term linguistic exposure and a minimal vocabulary. Dogs demonstrated a vowel bias rather than a consonant bias; this suggests that a small lexicon and regular linguistic exposure, plus mature auditory processing, do not lead to consonant bias emergence. Overall, these chapters suggest that dog models can be useful for broad questions about systems underlying speech perception and about the role of language exposure in the development of certain speech perception processes. However, the studies faced limitations due to a lack of knowledge about dogs’ underlying cognitive systems and linguistic exposure. More fundamental research is necessary to characterize dogs’ linguistic exposure and to understand their auditory, attentional, and linguistic processes to ask more specific comparative research questions.Item Taurine: An Indispensable Ingredient in the Development of Sustainable Aquafeeds(2013) Watson, Aaron Mackenzie; Place, Allen R.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Aquaculture as a global industry is at a crossroad; increased production cannot rely on the unsustainable harvest of forage fish for feed production. The use of fishmeal and fish oil as components in feeds for aquaculture, most notably for high value marine carnivores must be reduced or eliminated. The most promising and sustainable sources of replacement feed must be plant derived, such as soybean meal, wheat flour, and corn gluten along with dozens of other plant derived sources. Likewise for fish oil the most promising sources are plant oils such as soybean and canola oil supplemented with necessary omega-3 fatty acids. This work was undertaken to examine the effects of switching marine carnivores from fishmeal-based feeds to fishmeal-free, plant-based diets. The majority of this research has been conducted with cobia, Rachycentron canadum, a promising species for intensive aquaculture due to its rapid growth rates, high disease resistance, and lack of a major commercial fishery as competition. A variety of plant proteins, plant protein blends and alternative lipid sources were examined for digestibility and efficacy as fishmeal replacement sources in regards to their effects on growth rates, feed conversion, and a range of physiological characteristics. This work has explored the hypothesis that marine carnivores have lost the ability to synthesize taurine, a non-protein amino acid, in sufficient quantities and must therefore be supplied through the diet, and should be considered essential for all marine carnivores. By measurement of gene expression of the genes in taurine biosynthesis, this work shows that cobia do not possess the ability to regulate taurine biosynthesis confirming taurine must be supplied through the diet. Overall, this work has developed multiple plant protein-based feeds that perform equivalently or better than commercial and commercial-like diets. Taurine has been shown to be an essential ingredient when seeking to reduce or preferably, eliminate fishmeal and thereby making aquaculture sustainable in providing protein to meet the world's growing population.Item Electroencephalography (EEG) and measures of nociception in cattle(2013) Drnec, Kim Ann; Stricklin, William R; Simon, Jonathan Z; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The first known bovine laser evoked potential (LEP), an EEG response to noxious laser heat stimuli, was measured in 2-3 year old Holstein cows (n=5). The amplitude of the bovine LEP correlated significantly (P<. 05) with behavior scores, the surrogate for self-reporting in human studies. Importantly, and comparable to human studies, the LEP occurs at a latency within which it is considered that cortical potentials reflect increasingly complex cognitive processes, rather than those that are reflexive and non-conscious. Differences between the bovine and human LEP were also determined, that cannot be fully explained at this time. The lack of standardization for large animal EEG-investigations is problematic regarding data sharing across labs. A proposed standard method, for collecting and processing EEG in cattle was developed and is presented. Compared to human studies, signal processing of bovine data required significantly more stringent rejection criteria for data analysis. For example, while wavelet denoising is often used in human EEG; it was found essential for extracting a bovine LEP. In addition, explicitly addressing whether of not cortical potentials were being recorded was necessary to provide foundational background knowledge of bovine EEG. To this end, EEG was recorded under conditions designed to simulate the suppression and excitation of the primary visual cortex, as is measured in humans using eyes-open and eyes-closed. The simulation contrasted a dark and light environment. I propose this protocol to be used in the future large animal studies to verify that cortical potentials are being measured before EEG data recording. My results demonstrate that bovine EEG is a useful bovine cognitive science method, but more sophisticated signal processing techniques are needed to ameliorate issues of artifact. Lowered signal to noise ratios is considerably problematic for evoked response studies in large animals. Importantly, this research determined that a bovine LEP is measurable, and by analogy to human perceptual studies, I contend this demonstrates the cow experiences both the sensation and perception of noxious stimulus as painful.Item Dynamics of dietary methylmercury uptake and maternal transfer in estuarine forage fish(2012) Stefansson, Emily Suzanne; Heyes, Andrew; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Dietary methylmercury (MeHg) uptake in relation to fish lifestage, species, and level of exposure are poorly understood in lower trophic levels, particularly in estuarine species. Furthermore, little is known about the transfer of accumulated MeHg from female to offspring. Dietary MeHg accumulation, as well as growth and survival, were compared in two species of estuarine forage fish: Cyprinodon variegatus and Menidia beryllina. Results indicated that M. beryllina was more sensitive to dietary MeHg exposure than C. variegatus. Growth rate and the level of dietary exposure strongly influenced MeHg tissue concentrations in both species. In a second experiment, the source of maternally transferred MeHg was examined using a stable mercury isotope approach. A significant portion of Hg in eggs was from the burden stored in female tissues, suggesting that historical mercury exposure can be important in the context of maternal transfer.Item COMMUNICATING IN SOCIAL NETWORKS: EFFECTS OF REVERBERATION ON ACOUSTIC INFORMATION TRANSFER IN THREE SPECIES OF BIRDS(2011) Blumenrath, Sandra; Dooling, Robert J; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In socially and acoustically complex environments the auditory system processes sounds that are distorted, attenuated and additionally masked by biotic and abiotic noise. As a result, spectral and temporal alterations of the sounds may affect the transfer of information between signalers and receivers in networks of conspecifics, increasing detection thresholds and interfering with the discrimination and recognition of sound sources. To this day, much concern has been directed toward anthropogenic noise sources and whether they affect the animals' natural territorial and reproductive behavior and ultimately harm the survival of the species. Not much is known, however, about the potentially synergistic effects of environmentally-induced sound degradation, masking from noise and competing sound signals, and what implications these interactions bear for vocally-mediated exchanges in animals. This dissertation describes a series of comparative, psychophysical experiments in controlled laboratory conditions to investigate the impact of reverberation on the perception of a range of artificial sounds and natural vocalizations in the budgerigar, canary, and zebra finch. Results suggest that even small reverberation effects could be used to gauge different acoustic environments and to locate a sound source but limit the vocally-mediated transfer of important information in social settings, especially when reverberation is paired with noise. Discrimination of similar vocalizations from different individuals is significantly impaired when both reverberation and abiotic noise levels are high, whereas this ability is hardly affected by either of these factors alone. Similarly, high levels of reverberation combined with biotic noise from signaling conspecifics limit the auditory system's ability to parse a complex acoustic scene by segregating signals from multiple individuals. Important interaction effects like these caused by the characteristics of the habitat and species differences in auditory sensitivity therefore can predict whether a given acoustic environment limits communication range or interferes with the detection, discrimination, and recognition of biologically important sounds.